Background correction of two-colour cDNA microarray data using spatial smoothing methods

Transcriptome Analysis and Cell Morphology of Vitis rupestris Cells to Botryosphaeria Dieback Pathogen Diplodia seriata

Diplodia seriata, one of the major causal agents of Botryosphaeria dieback, spreads worldwide, causing cankers, leaf spots and fruit black rot in grapevine. Vitis rupestris is an American wild grapevine widely used for resistance and rootstock breeding and was found to be highly resistant to Botryosphaeria dieback. The defense responses of V. rupestris to D. seriata 98.1 were analyzed by RNA-seq in this study. There were 1365 differentially expressed genes (DEGs) annotated with Gene Ontology (GO) and enriched by the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The DEGs could be allocated to the flavonoid biosynthesis pathway and the plant–pathogen interaction pathway. Among them, 53 DEGs were transcription factors (TFs). The expression levels of 12 genes were further verified by real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). The aggregation of proteins on the plasma membrane, formation variations in the cytoskeleton and plasmodesmata and hormone regulations revealed a declined physiological status in V. rupestris suspension cells after incubation with the culture filtrates of D. seriata 98.1. This study provides insights into the molecular mechanisms in grapevine cells’ response to D. seriata 98.1, which will be valuable for the control of Botryosphaeria dieback.

Evaluating the effect of various background correction methods regarding noise reduction, in two-channel microarray data

In this work, two novel background correction (BC) methods, along with several commonly used ones, are evaluated regarding noise reduction in eleven two-channel self-versus-self (SVS) hybridizations. The evaluation of each BC method is investigated under the use of four statistical criteria combined into a single measure, the polygon area measure. Overall, our proposed BC approaches perform very well in terms of the proposed measure for most of the cases and provide an improved effect regarding technical noise reduction.